BioJava in Jupyter Notebooks
This repository demonstrates how to run BioJava applications in a Jupyter Notebook and Jupyter Lab.
This project uses the Java Kernel developed by the BeakerX project, a collection of kernels that provide JVM support for Jupyter Notebook and Lab.
The nbviewer links below provide a non-interactive preview of notebooks and the launch links launch the notebooks in Jupyter Notebook and Jupyter Lab in your web browser using the Binder (mybinder.org) server (may be slow!).
|nbviewer||Jupyter Notebook||Jupyter Lab|
By combining BioJava code with Python data analysis, machine leanrning, and visualization tools in a Jupyter Notebooks, a workflow can be shared, reproduced, and reused.
Open a terminal window
Clone this repository
git clone https://github.com/sbl-sdsc/biojava-notebooks.git
Create a conda environment
conda env create -f binder/environment.yml
Activate the conda environment
conda activate biojava-notebooks
Launch Jupyter Notebook
After you are finished, deactivate the conda environment
Anytime you want to use the environment, activate it again and start Jupyter Notebook
To permanently remove the biojava-notebooks environment
conda remove --name biojava-notebooks --all
How to Contribute
Do you have an idea for a new notebook? Please file an issue.
To contribute a new notebook, fork this repository and create pull-requests.
Please follow the Ten Simple Rules for Reproducible Research in Jupyter Notebooks.